Human immunodeficiency virus type 1 (HIV-1) protease is essential for viral replication and has proved a very effective target for antiviral drugs to treat AIDS. But, the long term effectiveness of current AIDS therapy is confronted by the major challenge of rapid development of drug-resistant HIV. Multiple mutations accumulate in the protease in response to inhibitor therapy and produce resistance. The overall goal is to develop new antiviral protease inhibitors and therapeutic strategies to overcome the problem of drug- resistance. The overarching hypothesis is that improved knowledge of the molecular mechanisms for HIV resistance to protease inhibitors will aid in development of potent new therapeutic agents to combat drug resistant virus. Our kinetic and structural analysis has shown that protease mutations can produce inhibitor resistance by several mechanisms, including lower affinity for inhibitor due to mutations that alter the inhibitor binding site, and altered protease stability due to mutations that alter the dimer interface. The central design strategy is that inhibitors with improved polar interactions with conserved regions of HIV protease will be potent drugs for resistant HIV. Our analysis of HIV protease-inhibitor structures has demonstrated the importance of the conserved set of hydrogen bond interactions between main chain atoms of peptide analogs and the protease backbone atoms. Our crystallographic analysis shows that the earlier clinical inhibitors have fewer of these polar interactions and high affinity is achieved by van der Waals interactions with protease side chains, leading to sensitivity to mutations in the binding site. The new antiviral inhibitor darunavir (TMC114; UIC-94017) was designed and confirmed to include more hydrogen bonds with protease main chain atoms. Darunavir showed fewer changes than other clinical inhibitors on the structures and activities of mutant proteases, resulting in high potency, excellent resistance profile, and approval for AIDS salvage therapy in June 2006. Our design strategy was further verified by analysis of the antiviral inhibitors GRL-06579A and GRL-98065. The appearance of new resistance mutations, diverse mechanisms of resistance and adverse side effects of drugs necessitate the development of new non-peptide inhibitors to expand the repertoire and potency of antiviral agents for resistant HIV. This research integrates in vitro analysis of the crystal structures and enzymatic activities of HIV protease mutants, chemical synthesis, and antiviral studies in HIV-infected cells to design novel protease inhibitors in the combat against resistant HIV.